FRET Benchmark

This directory contains all the scripts to run the benchmark of the FRET_R Bayesian restraint, and the reference results.

Folder structure

• DATA:

  • GMM: Gaussian Mixture Models needed by model for linker flexibility
  • PDBs: Pdb with complex structure, one per chain
  • REFERENCE_RESULTS: reference results of benchmark
  • SCRIPTS: scripts to run and analyze the benchmark
    • ANALYSIS: scripts to analyze the results
    • BENCHMARK_LINKER: scripts to run the benchmark with model for linker flexibility
    • BENCHMARK_NOLINKER: scripts to run the benchmark without model for linker flexibility

• RESULTS_LINKER : directory where the results of benchmark with model for linker flexibility will be stored

• RESULTS_NOLINKER : directory where the results of benchmark without model for linker flexibility will be stored

How to run the benchmark

0. This is the ROOT directory.

1. PRELIMINARY. Compile IMP (any recent version should work - see below for the last known good IMP version). IMP git version develop-c47408c was used for the publication.

2. EXECUTION. Go to DATA/SCRIPTS/BENCHMARK_LINKER or DATA/SCRIPTS/BENCHMARK_NOLINKER where you will find the scripts to run the benchmark with or without using a model for linker flexibility, respectively. Then:

   • To run a specific test, run:

     ./do_test.sh ID

     where ID is an integer from 1 to 1280.

   • To run all tests, just use a bash loop:

     for((ID=1;ID<=1280;ID++)); do ./do_test.sh $ID; done

   • A sample SGE script to run all the tests on a cluster is also provided, as job.sh.

3. ANALYSIS. From the ROOT directory, do:

   • DATA/SCRIPTS/ANALYSIS/do_analysis.py RESULTS_LINKER linker.dat
   • DATA/SCRIPTS/ANALYSIS/do_analysis.py RESULTS_NOLINKER nolinker.dat
   • DATA/SCRIPTS/ANALYSIS/do_analysis_per_complex.py RESULTS_LINKER linker_per_complex.dat
   • DATA/SCRIPTS/ANALYSIS/do_analysis_per_complex.py RESULTS_NOLINKER nolinker_per_complex.dat

   Statistics will be written to the .dat files, which should be compared to the results in DATA/REFERENCE_RESULTS and to those published in Bonomi et al. "Determining protein complex structures based on a Bayesian model of in vivo FRET data", as follows.

   • linker.dat -> Table S2
   • nolinker.dat -> Table S3

Author(s): Max Bonomi

Version: 1.0

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version:

Testable: Yes.

Parallelizeable: Yes

Publications:

• M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. Determining protein complex structures based on a Bayesian model of in vivo FRET data. Mol Cell Proteomics 13, 2812-2823, 2014.